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Table 2 Type I retrocopy-exon acquisition events

From: Retrocopy contributions to the evolution of the human genome

Parent Gene/RetroGene Fig Evolutionary Event and possible consequences Evidence Hs Pan Pon Rhesus Marm
PPP1R14BLIMK2 1A-1 Retro adds PKC-activated phosphatase-1 inhibitor domain to LIM, Zinc binding, PDZ kinase gene at alternatively spliced C-terminal exon. 2 spliced mRNAs, 4 spliced ESTs Reviewed RefSeq 686 aa y but stop codon after 13 aa y but stop codon after 19 aa n n
CENTG2/CTGLF1 1A-2 Retro adds centaurin domain to C-terminal of cyclin gene,. 2 spliced mRNAs, 2 spliced ESTs 663 aa y but seq. gap Y y 3 and 63 bp insertion, but 3 in-frame stops, occurring after 450 aa n
C10ORF26/BCAP29 1A-3 14 aa alternative 3' exon sense orientation out of frame wrt coding region of parent 6 spliced ESTs 244 aa y 244 aa y 233 aa y 241 aa Not assembled
RPL32/RPS29 1A-4 Retro insertion triggered new alt spliced C-terminal exon for RPS29. Most of the retro became 3' UTR. 1 spliced mRNA, > 20 spliced ESTs 67 aa y 67aa y 67 aa y 64aa y 81 aa
MLTT6/AF1/BRPF3 1A-5 Retro contributed PHD/zinc finger with bromodomain. 3 spliced mRNAs, > 10 spliced ESTs 1205 aa y 1205 aa y 1205 aa y 1006 aa y 885 aa
ATP5/GPR142 1A-6 Retro swapped in C-terminal portion of GPCR. New ligand in primates? 2 spliced mRNAs, 2 spliced ESTs 462 aa y but frameshift early in ORF y but frameshift early in ORF y 462 aa y but frameshift early in ORF
RPL21/BRCA1 1B-1 Antisense internal cassette (alt spliced) exon inserted by retro. 1 spliced mRNA 1354 aa y 100% open y 100% open y 100% open n
CYCS/RORA 1B-2 Antisense alt. spliced internal cassette exon contributed by retro. Protein evidence in Swiss-Prot and PDB 1 spliced mRNA PDB 1N83,1SOX 556 aa y in frame stop in first 20 aa y 556 aa y late translational start (31aa shorter) y difficult to check ORF.
RRAS2/SCP2 1B-3 Antisense retro triggered shorter alternative transcript in apes. 2 spliced mRNAs, 3 spliced ESTs 332 aa y 332aa N n n
FLJ10324/KIAA0415 1B-3 Antisense, ancient 8 spliced mRNAs 807 aa y Seq gap y  
/HLA-F 1B-3 Antisense, alt. spliced C-terminus 2 spliced mRNAs 377 aa y   y  
EIF3S6/C6orf148 1B-4 Retro contributed internal 15 aa antisense exon. 2 spliced mRNAs, 5 spliced ESTs 238 aa y 100% open   y 100% open y no ORF splice site has indel
RPS15A/HK1 1B-5 Antisense retro triggered slightly later start via novel exon. Alternative translation initiation. Reviewed RefSeq. 1 spliced mRNA 2 spliced ESTs 905 aa y 905 aa y 100% open y 905 aa n/a
RPL24/DENN1B 1B-5 Primate specific antisense internal cassette exon generated short alt spliced transcript encoding 396 aa. Possible alternative translation initiation. 6 spliced mRNAs 396 aa y 396 aa y ORF ok but missing splice site y no start codon  
RPL18/CSMD3 1B-6 Antisense retro triggered different start via novel exon. 1 spliced mRNA 3667 aa seq gap f/s wrt human. y f/s wrt to human. Same as PPY  
  1. Examples of specific categories of retrocopy insertion events shown in Figure 2 with designation of parent gene. Genomic locations of the examples are cross-referenced in [see Additional File 1]. y; indicates presence of the retrogene in this species, n; indicates its absence, aa; amino acids in potential encoded entire protein, f/s; frame shift, wrt; with respect.